SAM4s bootloader not responding via usb

[talanfree]

Hello,
I am trying to communicate with sam4s on my custom board with simple commands given in section 24.5 in datasheet. Bootloader returns answer when is connected via UART. But when when i open terminal and try the same commands when connected to usb it doesn't return anything. USB is successfully enumerated and recognized as ttyACM0. I am running Ubuntu 15.10. Where am getting wrong?

[tsvoipio]

Check your master clock. An UART is much more tolerant toward inexact or varying clock frequency than USB.

--

-TV

[talanfree]

I am using external clock on XIN pin 12Mhz oscillator from TXC. I checked with a scope. It looks fine.
When USB is attached i can't communicate via UART. I guess it is switched correctly to USB.

[talanfree]

I've success with communication through USB. The solution is described in atmel
knowledge base
http://atmel.force.com/support/articles ... -ubuntu-PC

Does somebody know why reinitialize usb driver is needed?